Companies and charities that spend billions of pounds on research and development in the UK have said it is not their job to fill the gaps in university funding that will be left if the government's proposed cuts to the science budget go ahead.

The private sector spends around £13bn a year on R&D in the UK, and a significant portion is spent in partnership with universities to fund basic science or to turn ideas into commercial products. But all that investment is dependent on a strong, publicly funded university system, said company and charity chiefs.

"The private and charitable sector fund in the UK because we have a good partnership with government," said Mark Walport, director of the Wellcome Trust, a biomedical charity that says it spends around £600m a year on research. "We're not here in order to substitute for government, we can't do that. It sends the pharmaceutical community and the medical charity community an extremely bad signal if government cuts this area of funding. The government knows very well that the Wellcome Trust believes this is about synergy not substitution."

Mike Bushell, principal scientific adviser at the agrochemical company Syngenta, said it was "extremely unlikely" that private industry would step in to make up the shortfalls if the government cuts science funding. "The government does have to make cuts, everybody accepts that. It shouldn't be an across-the-board bacon slice, they have to set some clear national priorities and make sure that the impact of the investment they make really is felt as soon as it can in economic advantage for the country."

Syngenta spends around $1bn globally on R&D every year, around a fifth of that being spent in the UK. "We've got hundreds of individual collaborations on at any time, we fund about 50-60 PhD studentships at any one time across a range of different disciplines," said Bushell. "There are also good links between the best university departments and our research groups in the UK."

In 2008/09, the government supplied funding for university research to the tune of £3.3bn via the research councils and £2.2bn via the higher education funding councils, and most of this was for curiosity-driven science. Research council funding is distributed through competitive grants for specific research projects and it pays for equipment and PhD and postdoctoral students. Higher education funds are distributed to universities for basic infrastructure.

All government departments have been asked to prepare for cuts of 25% or more in their budgets as part of the government's austerity drive. Scientists have warned that such deep cuts to the UK's science infrastructure would have devastating long-term effects, forcing the country out of the "premier league" in many fields of research and leading to the loss of a generation of scientists from the UK. In a worst-case scenario, up to £1bn in total could be wiped off annual budgets.

Richard Barker, director general of the Association of the British Pharmaceutical Industry, said he would be "very disappointed" to see cuts of the order of 25% and warned that, even in such a scenario, there would be no reason for companies to step in to replace government funds. "The UK has been an attractive site for R&D because of the very strong basic science base. The vast majority of the UK research base is very competitive internationally and some of it is globally leading. Over a long-ish period of time [after spending cuts], companies would drift away. Any change you make to basic research, particularly basic life sciences research, the results will play out over 10-20 years."

Barker gave the example of monoclonal antibodies, targeted medicines that constitute a £25bn global market, which took several decades to get from the lab to market. "They were mapped out as possible therapies in 1975 in a laboratory in Cambridge, but it was only in the late 1990s and this century that they become substantial medicines. The companies would not have done that very basic research that the laboratory in Cambridge did."

If major cuts do occur and the UK's university base starts to erode, charities and companies are likely to look elsewhere to invest their money. At present the Wellcome Trust says it spends around 90% of its annual research budget in the UK, but Walport stressed the charity's global reach. "We have a clear strategy, which says we are a global funder and international help is an increasing part of our portfolio. I hope the UK will remain a powerful environment for conducting medical research."

Imran Khan, director of the Campaign for Science and Engineering, said: "Industry leaders have consistenly said their private sector investment depends on public support for science. If that support disappears, they will have no other choice but to look abroad for their raw materials: world class research and talented scientists and engineers."

He added: "As a nation we don't have any choice but to gear up to having a high-tech, high-skills economy. With our international competitors increasing their investment in science and engineering, this would be the worst possible time to lower our own ambitions – it could take decades to rebuild our technological base to its world-class status."

The comments by business and charity leaders echo the conclusions of a report, to be published next week, by Research Councils UK, which looks at the role of science in the UK's future prosperity. "Continued public investment in scientific endeavour is essential for the success of UK business and industry – and, more broadly, for a productive economy, a healthy society and a sustainable world. Estimates of the impact of research council spending on the UK's national output suggest that a cut of £1bn in annual spending would lead to a fall in GDP of £10bn," the report will say.

David Cairncross, a senior policy adviser at the Confederation of British Industry (CBI), said: "Publicly funded investment in both research and development has a multiplier effect, making the UK a more attractive location for businesses to invest. Any cuts which are made to university research funding should be skilfully managed to minimise the negative impact on business investment."

This article was amended on 8 October 2010. The original stated that the Wellcome Trust spends £450m a year on research, and that 80% of this is spent in the UK. These figures have been corrected.